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When a Pokémon is obtained in a trade, it oftentimes will not obey the player's commands if it is at too high a level and the player does not have the appropriate Badge or number of Badges. Having all eight Badges always makes all Pokémon obey the player. This rule stands to prevent players from trading in a high-leveled Pokémon trained on another game and easily beating the game.

So from what I understand the Pokemon has to be traded to disobey you. Hope I helped :)